Variant report

Variant	rs13217662
Chromosome Location	chr6:64238520-64238521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:64234904..64241405-chr6:64279564..64285170,9	MCF-7	breast:
2	chr6:64232325..64242084-chr6:64281113..64285530,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112245	Chromatin interaction
ENSG00000266680	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10943869	0.88[EUR][1000 genomes]
rs13200519	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13205487	0.86[EUR][1000 genomes]
rs1744134	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1744143	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1744153	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779739	0.85[EUR][1000 genomes]
rs1779777	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2025178	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2489272	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2622312	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2758244	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6916092	0.87[EUR][1000 genomes]
rs71534831	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7753325	0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13217662	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64237000-64238600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:64237000-64240600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:64237200-64238600	Enhancers	NH-A	brain
4	chr6:64237400-64238600	Flanking Active TSS	NHEK	skin
5	chr6:64237400-64238800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr6:64237600-64238800	Enhancers	GM12878-XiMat	blood
7	chr6:64237600-64238800	Flanking Active TSS	Hela-S3	cervix
8	chr6:64237600-64240400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:64237800-64238600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:64237800-64238800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:64237800-64238800	Enhancers	Pancreas	Pancrea
12	chr6:64237800-64239600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:64238000-64238600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:64238000-64239200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:64238200-64239200	Weak transcription	Fetal Intestine Small	intestine
16	chr6:64238200-64239200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:64238200-64239400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:64238200-64239400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:64238200-64239400	Weak transcription	Liver	Liver
20	chr6:64238200-64239400	Enhancers	HMEC	breast
21	chr6:64238400-64238600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr6:64238400-64239200	Enhancers	A549	lung
23	chr6:64238400-64239400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:64238400-64239400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:64238400-64239400	Weak transcription	Stomach Mucosa	stomach
26	chr6:64238400-64239400	Weak transcription	NHLF	lung
27	chr6:64238400-64239400	Weak transcription	Osteobl	bone
28	chr6:64238400-64239600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:64238400-64239600	Weak transcription	Small Intestine	intestine
30	chr6:64238400-64240200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr6:64238400-64241000	Genic enhancers	HepG2	liver

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